A model Catacomb 3 is a structured document containing text and
tables. The table contain parameter values, text and other tables.
The individual values can be numbers, selections from a list of
named options, or references to other models.
The structure that document takes (the types and labels for
entries in the tables) is set by a framework that sets out
what is possible for the particular class of model under
construction. The framework also contains extra information about
table entries. For example, it says what the units are for
numeric quantities and what type of sub-table is appropriate in
a particular place. Catacomb 3 allows you to edit models using
existing frameworks and also to define new frameworks.
There are three ways that tables are presented in the user interface:
they can be summarized as a page of text; they can be presented
as a form to fill in the field values; or they can be shown as
a combination of a diagram with a set of smaller forms for the
separate components. Any table can be shown in any form - which one
is best depends on the framework of the model.
When defining frameworks there are shortcuts built in that
make Catacomb 3 particularly suitable for building models that
can be represented as assemblies where the nodes can be connected
to each other in a variety of configurations.
Each node is a table and the framework
defines plugs and sockets that go with the table. Building a model
involves joining up nodes by connecting the plugs on one node to
matching sockets on other nodes.
This document gives an overview of the main model building
interfaces nd then briefly discusses the
component building process. The latter is covered in more detail
Model building interface
The images shows the main windows in Catacomb. Clicking
an image opens the full-sized version in a new browser window.
There are a lot of other dialogs and but these are the main ones
for building and running models. You can find information about
any component by right-clicking on it or using the help menu.
Assemblies - plugs and sockets
Assemblies are collections of
components connected together. Unlike Catacomb 2,
there are no special components that act as links. Instead, any component can
have sockets for receiving connections and plugs for making connections to
In this scheme, a simple link such as a wire is represented as
a component with two plugs (for the two
ends of the link) and no sockets.
Component design interface
The model building interface described above is for
making models using pre-defined components. For example, there is a
pre-defined ion channel framework within which you can build
models for a whole variety of different ion channels.
But if you want to define a framework for a new class of models, then
you need the model design interface. This is accessed by switching
to the "components" tab (top left) and is shown on the right.
The first thing about the component interafce is that it looks a
lot like the model building interface. Designing a new component
is very much like building a model, except that only certain built-in
items can be put into a component. These
Text - the first items of any model or framework are
always a short one-line tag for summarising what it is and then
a longer description. These do not affect any calculations, but
without them the framework is unlikely to be much use.
Fields - slots where the model builder will
insert a value. They can be numbers, true-false values,
items selected from a list or references to other models.
Tables - a another component of a different
Sets - the model builder can insert
several tables of the same type.
Quantified Lists - quantities of other items, as in a
recipe. When a quantified list is presented for model building
you see all the models of the corresponding type
in the workspace and can specify how much of each you want.
A typical application is in channel densities on a cell: you
can specify a mixture of channels as a quantified list
where the quantities are the densities of each channel type.
Sockets - access points for connections from other
Plugs - access points to connect to other
Icon - the icon to use for the component in diagrams.
|Component as an assembly